Carbohydrate-Active Enzymes Involved in the Secondary Cell Wall Biogenesis in Hybrid Aspen

Henrik Aspeborg; Jarmo Schrader; Pedro M. Coutinho; Mark Stam; Åsa Kallas; Soraya Djerbi; Peter Nilsson; Stuart Denman; Bahram Amini; Fredrik Sterky; Emma Master; Göran Sandberg; Ewa Mellerowicz; Björn Sundberg; Bernard Henrissat; Tuula T. Teeri

doi:10.1104/pp.104.055087

Published March 2005. DOI: https://doi.org/10.1104/pp.104.055087

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Figure 1.
Clustering using self-organizing maps of 450 genes. Genes with less than two valid data points in sections C to E or with a signal less than 2-fold higher in D than in A to C and E were filtered out.
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Figure 2.
Phylogenetic analysis of plant GTs from family GT8. Profile-aligned Populus sequences are in bold, and partial sequences are indicated. Subfamilies with at least one characterized enzyme are outlined by a thick black line and those without defined activities by a thin gray line.
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Figure 3.
Phylogenetic analysis of plant GTs from family GT43. Legend as in Figure 2.
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Figure 4.
Phylogenetic analysis of plant GTs from family GT47. Legend as in Figure 2.
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Figure 5.
Phylogenetic analysis of plant GTs from family GT61. Legend as in Figure 2.

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Table I.

Strictly D-specific genes encoding CAZymes: a selection of genes that passed both filter I and filter II

Ratios are presented in log₂ scale, and log₂ ratios >1 are in bold.

Gene^a	Sequence^a	EST^a	13.5 K Array^a					3 K Array^b	Xy versus Ph^c
Gene^a	Sequence^a	EST^a	A	B	C	D	E	3 K Array^b	Xy versus Ph^c
PttCesA1	FL	A064P24U	−6.41	−5.79	−0.30	1.26	−0.58	Yes	5.66
PttCesA1	FL	G109P08Y	−4.79	−4.41	−0.18	1.79	−0.70	NA	5.30
PttCesA3-1	FL	A040P09U	−4.77	−4.33	0.54	1.75	−1.64	Yes	5.04
PttCesA3-2	FL	G097P01U	−6.02	−5.45	−0.20	1.81	−0.32	NA	5.27
PttCesA3-2	FL	G103P13Y	−5.88	−5.59	−0.32	1.34	−0.29	NA	5.44
PttCesA9	Partial	G072P74Y	−6.03	−5.46	−0.08	2.62	−1.07	NA	6.11
PttCesA9	Partial	G072P58Y	−2.03	−1.70	0.03	1.48	0.33	NA	4.47
PttGT2A	Partial	B005P05U	−4.77	−4.77	−0.59	2.06	0.01	Yes	5.89
PttGT8B	FL	A065P67U	−5.91	−5.54	−1.32	2.24	−1.99	Yes	6.51
PttGT8B	FL	G069P14Y	−5.89	−5.11	−1.28	2.35	−1.90	NA	6.65
PttGT8C	FL	A073P75U	−4.74	−4.90	0.33	2.04	−1.61	Yes	5.66
PttGT8D	Partial	B004P07U	−6.69	−6.26	−1.65	1.98	−0.62	Yes	6.25
PttGT8D	Partial	G069P39Y	−4.41	−4.45	−1.48	2.30	−0.58	NA	5.93
PttGT8E	FL	G079P18Y	−1.39	−1.11	0.23	1.98	−2.19	NA	2.71
PttGT8E	FL	UB22CPE03	−0.81	−1.10	0.21	1.95	−2.51	NA	3.19
PttGT8F	Partial	G069P06Y	−2.39	−2.07	−0.74	2.36	−0.47	NA	4.98
PttGT31A	Partial	G133P32Y	−2.14	−1.97	0.86	2.02	−2.03	NA	3.10
PttGT43A	FL	B002P16U	−4.31	−4.25	0.33	1.79	−3.59	Yes	4.69
PttGT43B	FL	A027P19U	−5.05	−4.10	0.37	1.94	−2.32	Yes	4.76
PttGT47A	FL	A004P36U	−5.16	−5.24	−0.67	1.25	−2.03	Yes	5.06
PttGT47A	FL	A005P12U	−4.58	−4.75	−0.66	1.60	−2.05	Yes	4.89
PttGT47A	FL	A012P11U	−4.71	−4.71	−0.79	1.61	−1.89	Yes	5.26
PttGT47A	FL	G106P73.3pR	−4.06	−3.90	−0.57	2.02	−1.96	NA	4.36
PttGT47A	FL	G072P66.3pR	−3.36	−2.84	−0.38	2.29	−1.42	NA	1.33
PttGT47C	FL	A045P41U	−4.28	−4.03	−0.42	1.95	−0.20	Yes	5.29
PttGT47C	FL	A018P14U	−2.92	−2.80	−0.28	1.95	0.18	Yes	5.12
PttGT47C	FL	G099P90Y	−1.49	−0.95	0.23	1.66	−0.31	NA	4.51
PttGT47C	FL	I042P36P	−1.52	−1.82	0.06	2.39	0.15	NA	4.18
PttGT47D	Partial	G124P64Y	−1.10	−0.86	−0.04	1.88	−1.16	NA	2.56
PttCel9A	FL	A064P06U	−2.35	−1.94	0.02	1.49	0.15	Yes	2.69
PttXyn10A	FL	A020P21U	−2.53	−1.76	−0.49	2.00	0.60	Yes	3.43
PttGH17A	Partial	G083P33Y	−0.48	−0.65	0.10	1.55	−0.26	NA	−1.87
PttGH19A	FL	A044P10U	−6.73	−6.42	−1.15	0.95	−0.37	Yes	6.60
PttGH19A	FL	G066P41.5pR	−6.27	−5.75	−1.16	1.46	−0.74	NA	5.93
PttGH19A	FL	G063P44.3pR	−3.89	−3.49	−1.13	1.41	−0.63	NA	4.64
PttGH28A	Partial	A060P67U	−1.85	−1.87	−0.04	1.55	0.43	Yes	3.52
PttBGal35A	Partial	A066P74U	0.02	−0.20	−0.42	1.71	−1.58	Yes	1.19
PttGH51A	Partial	F025P61Y	−1.77	−1.80	−1.55	2.62	−0.73	NA	3.49

↵a Several genes are represented by more than one EST on the arrays. FL, Full-length sequence.
↵b Data published in Hertzberg et al. (2001). Yes/no, Gene was/was not up-regulated in the D zone; NA, not available because the EST was not represented on the array.
↵c Expression data for rows 1 to 7 have been published in Djerbi et al. (2004). Xy, Xylem; Ph, phloem.

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Table II.

Genes encoding CAZymes highly expressed during secondary cell wall formation: a selection of genes that passed filter I but did not fulfill the requirements of filter II

Ratios are presented in log₂ scale, and log₂ ratios >1 are in bold.

Gene^a	Sequence^a	EST^a	13.5 K Array^a					3 K Array^b	Xy versus Ph^c
Gene^a	Sequence^a	EST^a	A	B	C	D	E	3 K Array^b	Xy versus Ph^c
PttCesA2	FL	F120P33Y	−0.30	−0.82	0.70	1.16	0.87	NA	0.63
PttCesA2	FL	A020P56U	−0.34	−0.85	0.58	0.94	0.71	No	0.63
PttGT8A	Partial	A002P51.3pR	−3.44	−1.28	0.22	1.75	1.07	Yes	3.75
PttGT8A	Partial	A002P78U	−3.46	−1.38	−0.01	1.42	0.91	Yes	3.53
PttGT8G	Partial	A068P23U	−0.35	0.04	0.48	1.08	−1.39	No	1.22
PttGT8G	Partial	F056P93Y	−0.19	0.30	0.71	0.82	−0.63	NA	0.41
PttGT8H	Partial	G091P40Y	−1.02	−0.65	−0.04	1.04	1.84	NA	2.34
PttGT14A	FL	A002P61U	−1.89	−1.91	0.67	1.60	0.34	Yes	3.91
PttGT14B	FL	B005P04U	−2.75	−1.15	0.92	1.34	−1.64	Yes	2.57
PttGT31B	Partial	G108P23Y	−1.59	−1.10	0.62	1.51	0.20	NA	2.15
PttGT47B	FL	A006P34U	−1.51	−1.23	−0.26	1.95	−0.33	Yes	3.25
PttGT61A	Partial	G123P20Y	−0.41	0.14	0.85	1.02	0.29	NA	0.64
PttGT61A	Partial	A020P80U	−0.53	0.14	0.69	0.80	0.03	No	0.59
PttXET16L	Partial	UB27CPD07	0.00	−0.53	0.02	1.42	1.10	NA	−0.11
PttBGal35B	Partial	G079P88Y	−3.55	−3.72	0.69	1.23	0.94	NA	3.34
PttBGal35B	Partial	G107P47Y	−3.48	−4.20	0.75	1.24	1.07	NA	3.16

↵a Several genes are represented by more than one EST on the arrays.
↵b Data published in Hertzberg et al. (2001). Yes/no, Gene was/was not up-regulated in the D zone; NA, not available because the EST was not represented on the array.
↵c Expression data for rows 1 and 2 have been published in Djerbi et al. (2004). Xy, Xylem; Ph, phloem.

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Table III.

Closest Arabidopsis homologs to the Populus CAZymes and published secondary wall-related expression data from other relevant plants

Gene	Homolog	Published Expression Data		Cotton
Gene	Arabidopsis	Arabidopsis^a	Zinnia	Cotton
PttGT2A CSL	At5g03760		Demura et al. (2002)
PttCesA1	At5g44030		Milioni et al. (2002)	Pear et al. (1996)
PttCesA2	At4g39350			Li et al. (2002)
PttCesA3-1	At4g18780	S1 and S4	Demura et al. (2002)	Pear et al. (1996)
PttCesA3-2	At4g18780	S1 and S4	Demura et al. (2002)	Pear et al. (1996)
PttCesA9	At5g17420	S1
PttGT8A	At4g33330
PttGT8B	At3g18660		Demura et al. (2002)
PttGT8C	At3g18660		Demura et al. (2002)
PttGT8D	At5g54690
PttGT8E	At1g19300
PttGT8F	At1g19300
PttGT8G	At3g02350
PttGT8H	At3g62660
PttGT14A	At3g03690
PttGT14B	A1gt71070
PttGT31A	At3g14960
PttGT31B	At1g05170	S1	Demura et al. (2002)
PttGT43A	At2g37090			Zhao et al. (2001)
PttGT43B	At2g37090	S1 and S4
PttGT47A	At1g27440
PttGT47B	At3g45400
PttGT47C	At2g28110		Demura et al. (2002)
PttGT47D	At5g61840
PttGT61A	At5g55500
PttCel9A	At5g49720	S1	Demura et al. (2002)
PttXyn10A	At1g58370		Demura et al. (2002)
PttGH16L	At1g14720	S1		Ji et al. (2003)
PttGH17A	At4g14080
PttGH19A	At3g16920
PttGH28A	At3g42950
PttBGal35A	At5g63800			Zhao et al. (2001)
PttBGal35B	At3g13750
PttGH51A	At3g10740		Demura et al. (2002)

↵a Data published by Oh et al. (2003). S1, Xylem up-regulated genes; S4, control up-regulated genes.

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Table IV.

Percentage identities/positives of the protein sequences of CesA proteins identified in poplar, Arabidopsis, barley, and rice

Gene sequences were retrieved from the Stanford Web site (http://cellwall.stanford.edu). Boldface indicates genes involved in secondary cell wall synthesis (data from Taylor et al., 2000, 2003; Joshi, 2003; Tanaka et al., 2003; Burton et al., 2004; Djerbi et al., 2004). At, Arabidopsis; Ptr, P. tremuloides; Hv, barley; Os, rice.

Gene	P. tremula × tremuloides (Ptt)/P. trichocarpa
Gene	CesA1	CesA2	CesA3-1	CesA3-2	CesA4	CesA5^a	CesA7^a	CesA8^a	CesA9^a
AtCesA1	62/74	62/74	61/71	61/72	61/73	68/78	68/80	83/89	62/72
AtCesA2	59/70	74/81	57/71	56/69	77/83	62/74	63/76	61/73	61/72
AtCesA3	63/74	62/77	61/72	60/71	62/76	81/87	79/86	68/78	65/74
AtCesA4	72/79	58/70	64/75	62/73	57/69	61/71	62/73	61/72	61/70
AtCesA5	60/72	73/80	56/69	57/70	75/80	63/75	63/75	61/73	60/71
AtCesA6	61/73	76/84	56/69	57/70	79/85	63/75	63/75	61/73	60/71
AtCesA7	62/73	62/74	61/72	61/72	61/73	65/74	66/76	63/74	81/86
AtCesA8	64/74	57/70	80/87	79/87	56/69	59/70	60/72	60/71	60/71
AtCesA9	59/72	76/84	56/69	56/70	77/84	64/74	62/76	61/73	60/71
AtCesA10	60/73	60/73	60/72	59/71	60/72	66/77	67/79	79/85	60/71
PtrCesA1	63/74	56/69	91/93	92/92	55/69	57/69	59/71	59/70	59/71
PtrCesA2	62/71	62/73	60/72	58/70	61/72	65/75	66/76	63/73	88/89
PtrCesA3	85/85	57/69	63/74	60/70	57/67	60/71	63/73	61/72	62/71
PtrCesA4	61/73	63/76	60/71	60/72	61/74	68/78	67/78	94/94	63/74
PtrCesA5	60/71	62/74	58/69	57/69	63/74	90/90	80/85	67/77	64/72
PtrCesA6	61/72	66/76	60/72	58/69	66/76	66/76	66/77	65/76	63/73
PtrCesA7	60/70	76/82	55/67	55/68	88/88	65/77	65/78	62/74	62/73
HvCesA1	61/71	62/75	58/70	58/70	61/73	75/83	76/84	67/77	63/72
HvCesA2^b	60/71	65/75	58/71	56/68	65/75	65/75	64/76	63/75	62/72
HvCesA3^b	61/72	61/74	59/71	58/70	61/73	76/82	77/84	67/76	64/73
HvCesA4^b	71/76	61/72	67/76	64/71	60/72	63/73	64/74	66/74	64/72
HvCesA5/7^b	68/79	65/79	78/85	78/86	65/79	67/79	67/79	67/78	65/76
HvCesA6	62/74	62/74	61/72	60/71	62/73	67/77	68/79	80/86	62/72
HvCesA8^b	68/81	72/81	71/82	68/80	71/81	78/85	78/84	74/83	82/85
OsCesA1	62/73	61/72	61/71	59/70	61/72	68/78	69/80	81/87	62/72
OsCesA2	62/73	63/76	59/70	59/71	63/75	78/84	78/84	68/78	65/74
OsCesA3	62/73	68/79	58/70	58/70	67/78	66/76	65/76	66/77	64/74
OsCesA4	62/73	67/81	74/81	74/81	66/80	60/72	61/73	60/71	59/70
OsCesA5	62/73	68/78	58/70	58/70	68/78	66/76	65/76	65/77	64/74
OsCesA6	61/72	66/76	58/71	57/70	66/76	66/76	65/78	64/76	62/73
OsCesA7	70/76	57/69	62/72	60/69	56/66	60/70	62/73	62/71	62/71
OsCesA8	61/71	63/76	59/70	58/70	62/73	78/84	78/84	68/77	64/73
OsCesA9^b	71/83	77/86	71/84	70/83	77/85	74/84	75/85	71/82	71/82